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<h4>Run Analysis </h4>
<hr>Run Analysis contains initializing parameters along with the steps involved 
in the group ICA.
<ul>
	<li>After the Setup ICA analysis is done click on the <i>Run analysis</i> 
	button, a screen will pop up asking you to select the parameters file. The 
	parameters file is the same file where you entered all the analysis 
	information. It is named with suffix 'ica_parameter_info.mat'. </li>
	<li>Once the parameter file is selected a figure (Figure 1) will pop up 
	showing the options for run analysis. The options are described below:<dl>
		<dt>All*** </dt>
		<dd>You can run all the group analysis steps at once or you have to 
		select each step in the order like after initialize parameters step 
		followed group data reduction step. </dd>
		<dt>Initialize Parameters </dt>
		<dd>Parameters are initialized in this step. </dd>
		<dt><a href="icatb_data_reduction.htm">Group data reduction</a> </dt>
		<dd>
		<ul>
			<li>Each subject's data is reduced. </li>
			<li>PCA is used as the data reduction step. </li>
			<li>After each subject's data is reduced they are concatenated into 
			groups and put through another data reduction step. </li>
		</ul>
		</dd>
		<dt><a href="icatb_calculate_ica.htm">Calculate ICA</a> </dt>
		<dd>The reduced data from the data reduction stage is plugged into the 
		ICA algorithm. </dd>
		<dt><a href="icatb_back_reconstruct.htm">Back Reconstruction</a> </dt>
		<dd>Regular - Individual subject image maps and time courses are 
		computed using both the results from the ICA stage and from the data 
		reduction stage. </dd>
		<dd> Spatial-temporal regression - The aggregate components and the original data are used to compute the individual subject components. </dd>
		<dt><a href="icatb_scaling_components.htm">Calibrate Components</a> </dt>
		<dd>Scaled image maps and time courses are computed using the individual 
		image maps and time courses. </dd>
		<dt>Group Stats </dt>
		<dd>Statistical methods are used to obtain group results. </dd>
	</dl>
	</li>
	<li>Results during each of the steps are printed to the MATLAB command 
	window. Before the group analysis can take place the parameters file must be 
	initialized. At this stage variables that were entered through the GUI are 
	parsed and initialized as needed for the group ICA analysis. Error checking 
	is also performed so that mistakes can be caught before the analysis starts. </li>
	<li>All the analysis information is also stored in a log file 
	('_results.log'). This file gets appended each time you run the analysis 
	with the same name to the prefix of the output files in the <a href="icatb_setup_ica.htm">
	<em>Setup ICA</em></a> analysis step. </li>
</ul>

<b>Note:</b>
<ul>
	<li>You need not run the whole analysis if you have changed the scaling 
	method or ICA algorithm as data reduction is the time consuming step for 
	large analysis. For running the analysis with changed scaling method, you 
	need to select 'Parameter Initialization', 'Calibrate Components' and 'Group 
	Stats' one at a time. For running the analysis with changed ICA algorithm, 
	you need to run all the steps except the data reduction. </li>
	
	<li> By default, the component spatial maps and time courses will be 
	compressed to a zip file according to their viewing set name like subject 1 
	session 1, mean for session 1, etc. The variable used for compressing is 
	ZIP_IMAGE_FILES (See <a href="icatb_defaults.htm">defaults</a>).
	</li>
	
	<li> <a href="icatb_displayGUI.htm">Display GUI</a> will open automatically 
	after the stats step is completed. You can turn off this option by changing 
	variable OPEN_DISPLAY_GUI to 0.
	</li>
</ul>

<p class="style1"> Figure 1: Run Analysis </p>
<p class="style1"> <img src="images/icatb_run_analysis.jpg"> </p>

<p>After the analysis is complete, the analysis information can be viewed using 
the <i><a href="icatb_analysis_info.htm">Analysis Info</a></i> 
button.</p>

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